You have to plan ahead for this one. You need to book a tour in advance and are taken by boat to the secluded, monkey-filled island where the underground river is. 

It's worth the effort. The sea and islands themselves are pristine and beautiful, and the caves themselves are a true natural wonder. I am always amazed by the sounds of life within caves and the well-preserved nature of these, with no artificial lights installed, makes it hugely important. Worth visiting and supporting.